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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 34 |
1 files changed, 34 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 92c0692f45..9b819d1a23 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15247,6 +15247,40 @@ database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.") (license license:expat))) +(define-public lofreq + (package + (name "lofreq") + (version "2.1.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/CSB5/lofreq") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qssrn3mgjak7df6iqc1rljqd3g3a5syvg0lsv4vds43s3fq23bl")))) + (build-system gnu-build-system) + (arguments + '(#:test-target "bug-tests" + #:tests? #false)) ; test data are not included + (inputs + `(("htslib" ,htslib) + ("python" ,python-wrapper) + ("zlib" ,zlib))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("which" ,which))) + (home-page "https://csb5.github.io/lofreq/") + (synopsis "Sensitive variant calling from sequencing data ") + (description "LoFreq is a fast and sensitive variant-caller for inferring +SNVs and indels from next-generation sequencing data. It makes full use of +base-call qualities and other sources of errors inherent in +sequencing (e.g. mapping or base/indel alignment uncertainty), which are +usually ignored by other methods or only used for filtering.") + (license license:expat))) + (define-public python-pyliftover (package (name "python-pyliftover") |